Promethease Report

This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...

discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...

rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...

23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group TNF-alpha (TNF) protein levels [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]

Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...

rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...

This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...

rs12150220 is a SNP in the NLRP1 gene, which encodes the NACHT leucine-rich-repeat protein 1. SNPs in this gene may be involved in higher risk for several autoimmune diseases. In a study investigating large patient cohorts from six different autoimmune diseases, including autoimmune Addison's disease (n=333 patients), type-1 diabetes (n=1086), multiple sclerosis (n=502), rheumatoid arthritis (n=945), systemic lupus erythematosus (n=156) and juvenile idiopathic arthritis (n=505), plus 3273 healthy controls, the rs12150220(A) allele was associated with higher risk for both autoimmune Addison's disease (odds ratio 1.25, CI: 1.06-1.49, p = 0.007) and type-1 diabetes (odds ratio 1.15, CI: 1.04-1.27, p = 0.005). [OMIM:NLR FAMILY, PYRIN DOMAIN-CONTAINING 1; NLRP1]

rs3732378 VAL249ILE is tightly linked to neighboring rs3732379 THR280MET The protein receptor with both variant amino acids is known as CX3CR1-M280. the minor alleles of this pair are associated with *more rapid progression to full-blown AIDS and probably increased susceptibility to HIV infection *reduced risk of acute coronary events *increased risk of age related macular degeneration [OMIM:?]

rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...

rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...

rs1136287, also known as Met72Thr, is a SNP in the PEDF gene. Analysis of 86 Taiwanese Chinese patients with wet age related macular degeneration (ARMD) found the (T) allele to be more frequent in patients than in controls (50% vs 31%; p =.0005). The rs1136287(T;T) genotype was also more prevalent in patients than in controls (odds ratio 3.9, p = .0015).

linked to blindness in age related macular degeneration rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [GWAS:None]

linked to blindness in old age rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [PharmGKB:Non-Curated GWAS Results: Complement factor H polymorphism in age-related macular degeneration (Initial Sample Size: 96 cases, 50 controls; Replication Sample Size: NR; Risk Allele: rs380390-C).] [OMIM:EXCISION-REPAIR CROSS-COMPLEMENTING, GROUP 6; ERCC6] [GWAS:Age-related macular degeneration]

may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]

rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A, I62V, or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs. rs800292 was associated with polypoidal choroidal vasculopathy (PCV) in a study of 130 Japanese patients. age related macular degeneration Susceptibility genes for age-re...

rs11200638, a SNP in the HTRA1 promoter, is associated with a 10 fold increased risk of wet age related macular degeneration in Japanese and Caucasian populations. Further confirmed . The genotype at highest risk is (A;A). Note that this SNP is completely predictive (ie is in perfect linkage disequilibrium) with rs10490924, thus the status of one predicts the status of the other. A 2011 meta-analysis concluded that rs11200638(A;G) and (A;A) carriers had 2.243 and 8.669 times the risk of developing AMD, respectively, when compared with those who carry the (G;G) genotype. rs10490924 and rs11200638 defined 2 significant haplotypes associated with increased risk of neovascular AMD. show that rs11200638 has no significant impact on HTRA1 promoter activity in three different cell lines, and HTRA...

rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and R131H. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...

23andMe blog females with one copy of rs5968255(C) progressed from HIV infection to AIDS more slowly with an average of eight years, nearly four times more than females with no copies or males. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? HIV Progression

this snp is on the 23andMe microarray but lacks a dbSNP identifier. discussed in the 23andMe blog *II +/+: Not resistant to HIV infection; shows average time of progression to AIDS after infection. *DI Delta32/+: Not resistant to HIV infection but may have slower progression to AIDS after infection. *DD Delta32/Delta32: Resistant to infection by the most common strain of HIV people usually encounter, though protection is not complete. Article also seems to discuss rs333 (aka CCR5Delta32) Resistance to HIV/AIDS

rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...

rs2076530(A) was estimated to double the risk of developing sarcoidosis, at least as based on a study of Caucasians. Although by itself it was not associated with increased risk for sarcoidosis in a population of African descent, this allele was part of a disease-associated haplotype. The rs2076530 SNP has also been investigated for associations with multiple sclerosis, Type-1 diabetes, SLE, and rheumatoid arthritis, but any association seen has apparently been due to carryover effects from nearby major histocompatibility haplotypes. rs2076530(A;A) associated with a risk of sensitization towards Der f allergies (Odds ratio; 1.55, p = 0.0060) [OMIM:BUTYROPHILIN-LIKE PROTEIN 2; BTNL2] [GWAS:Sarcoidosis]

This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...

rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...

While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the promoter region of the EIF2AK2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs2254958(C). The odds ratio is reported to be 1.61 (CI: 1.02-2.55) for rs2254958(C;C) homozygotes, and 1.24 (CI: 0.80-1.93) for rs2254958(C;T) heterozygotes, compared with ...

This SNP has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: CETP V405 valine homozygosity (GG genoty...

rs3025786 is a SNP in the presenilin 1 PSEN1 gene. A study of a Spanish case-control sample of 1,183 individuals showed rs3025786 was associated with Alzheimer's disease in an ApoE-specific manner: more specifically rs3025786(C) allele carriers have a decreased AD risk among carriers of the ApoE4 allele.

In APP source Detected in 1 patient with 2 ischemic strokes and myocardial infarction. No family history; no amyloid deposition. The variant also makes developing Alzheimer's disease four times less likely across all age groups. 'It confers extraordinarily strong protection,' said Stefansson. source http://www.decodeyou.com/decode-genetics-discovers-mutation-conferring-protection-against-alzheimers-disease-and-cognitive-decline-in-elderly/ http://blog.personalgenomes.org/2012/08/01/the-predominant-variant-of-the-app-gene-greatly-increases-risk-for-alzheimers-disease-and-cognitive-decline/

rs3825776, a SNP in the region of the LIPC gene on chromosome 15, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs3825776(G) is 1.34 (CI: 1.12 - 1.46).

rs2814707 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs3849942. In this study, the reported odds ratio for rs2814707(A) was 1.22 (CI: 1.15 - 1.30, p = 4.72 x 10e-10). The odds ratio for the minor rs2814707(A) allele was 1.16 (p=7.45x10e-9). 23andMe blog rs2814707(T) 1.16x odds of ALS rs12608932(C) 1.2x odds of ALS [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 5.2 (1.8, 16.7)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [OMIM:?]

rs3849942 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs2814707. In this study, the reported odds ratio for rs3849942(A) was 1.22 (CI: 1.15 - 1.30, p = 4.64 x 10e-10). The odds ratio for the minor rs3849942(A) allele was 1.15 (p=1.01x10e-8). From a study of 405 Finnish patients with ALS, rs3849942 was found within a 42 SNP haplotype associated with highly increased (p = 7 x 10e-33) risk when patients with familial ALS were compared to controls (odds ratio of 21.0, CI: 11.2-39.1). This haplotype overlapped with a region reported (by others) to associate with risk for frontotemporal dementia. In terms of population attributable risk, for the 93 patients with familial ALS, this 9p21 locus accounts for 38% and that of rs1304801...

This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...

discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...

A common variant on chromosome 9p21 affects the risk of myocardial infarction, and is further discussed in this blog post 23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 9q21.3; Reported Gene(s): CDKN2A, CDKN2B; Risk Allele: rs1333040-T); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 6] [GWAS:Intracranial aneurysm]

Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs9298506(A) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.28 (CI:1.20-1.38, p=1.0e-06). Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 8q11.23-q12.1; Reported Gene(s): SOX17; Risk Allele: rs9298506-A); (p-value= 0.000000002).This variant is associated with Intracranial aneurysm.] [OMIM:?] [GWAS:Intracranial aneurysm]

SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6). In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10^–4), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10^-4) in Graves ophthalmopathy patients. A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded t...

rs30187 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. Each T allele appears to increase the odds by about 1.4x (p=3.4x10e-10). A study of 872 Korean patients found that each T allele was associated with 1.5x higher odds of ankylosing spondylitis. [GWAS:None]

rs10865331 is a SNP in chromosomal region 2p15. After initial GWAS reports linked this SNP to ankylosing spondylitis (AS), a follow-up study in 456 Spanish patients replicated the association between the rs10865331(A) allele and higher risk for AS (p = 0.039). In a 2010 report, the AA genotype was associated with 1.3x odds of ankylosing spondylitis, and the GG genotype with 0.8x odds, compared to the AG genotype. [OMIM:?] [GWAS:Ankylosing spondylitis]

A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....

rs11209032 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.3 (p=7.5x10e-9). rs11209032 and rs1495965 no significant association with systemic sclerosis [OMIM:?]

rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...

rs9272346 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes, 18.52 (CI 12.69-27.03). Note that the (A) allele is the most common in various human populations; instead of labeling (A) as a risk allele, we could consider the (G) allele protective. Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Curated GWAS ...

This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...

This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common form...

Asthma

rs37973 is a SNP in the promoter region of the glucocorticoid induced transcript 1 GLCCI1 gene on chromosome 7. Based on 4 populations totaling 900+ asthma patients, the rs37973(G) allele was associated (p = 0.0007, pooled data) with lower amounts of improvement of lung function in response to inhaled glucocorticoids such as budesonide. The mean (±SE) increase in forced expiratory volume in 1 second (FEV1) in treated rs37973(G;G) patients was about one third of that seen in rs37973(A;A) patients (3.2±1.6% vs. 9.4±1.1%). Based on dividing the response into highest vs lowest quartiles of response, the allelic odds ratio of falling into the lowest responding quartile based on an additive genetic model was calculated to be 1.52 (CI: 1.13 - 2.03). Genotype accounted for about 7% of overall inha...